Expression profile of Urothelial carcinoma of the urinary bladder (UCB) or bladder cancer from Blood
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PROVIDER: PRJNA574646 | ENA |
REPOSITORIES: ENA
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Project description:The main aim of this study was to assess the changes in blood gene expression in UCB patients and to identify genes serving as biomarkers for UCB diagnosis and progression. Our study characterized the comprehensive expression profile of UCB and highlighted differences in expression patterns between UCB and healthy control
2020-01-24 | GSE138118 | GEO
Project description:Thiele2013 - Urinary bladder urothelial cells
The model of urinary bladder urothelial cells metabolism is derived from the community-driven global reconstruction of human metabolism (version 2.02, MODEL1109130000
).
This model is described in the article:
A community-driven global reconstruction of human metabolism.
Thiele I, et al
.
Nature Biotechnology
Abstract:
Multiple models of human metabolism have been reconstructed, but each represents only a subset of our knowledge. Here we describe Recon 2, a community-driven,
consensus 'metabolic reconstruction', which is the most comprehensive representation of human metabolism that is applicable to computational modeling. Compared
with its predecessors, the reconstruction has improved topological and functional features, including ~2x more reactions and ~1.7x more unique metabolites. Using
Recon 2 we predicted changes in metabolite biomarkers for 49 inborn errors of metabolism with 77% accuracy when compared to experimental data. Mapping metabolomic
data and drug information onto Recon 2 demonstrates its potential for integrating and analyzing diverse data types. Using protein expression data, we automatically
generated a compendium of 65 cell type-specific models, providing a basis for manual curation or investigation of cell-specific metabolic properties. Recon 2 will
facilitate many future biomedical studies and is freely available at http://humanmetabolism.org/.
This model is hosted on BioModels Database
and identified by: MODEL1310110035
.
To cite BioModels Database, please use: BioModels Database: An enhanced,
curated and annotated resource for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer
to CC0 Public Domain Dedication
for more information.
2005-01-01 | MODEL1310110035 | BioModels
Project description:Purpose: The goals of this study are to compare 1. The transcription profile in KDM6A wildtype and KDM6A mutated urothelial bladder carcinoma. 2. The transcriptional changes in KDM6A mutated urothelial bladder carcinoma upon EZH2 inhibitor treatment.
2017-03-01 | GSE92723 | GEO
Project description:At diagnosis approximately 75% of bladder urothelial carcinomas are non muscle invasive bladder cancers (Ta, T1 and Tis), 20% are muscle invasive bladder cancer (T2-T4) and 5% are already metastatic. Non muscle invasive bladder cancers are characterized by tumor recurrence in 60% to 85% of cases and, therefore, long-term followup is needed. The current standard methods to detect and monitor bladder cancer are cystoscopy and cytology. Cystoscopy is an invasive method and cytology is hampered by low sensitivity, especially for low grade tumors. So there is need to develop reliable and noninvasive methods to detect and predict bladder cancer biological behavior. So we have performed high density oligonucleotide microarray for discovery of new molecular markers to diagnose and predict the outcome of bladder cancer. Under an ethical guideline of Chhatrapati Shahuji Maharaj Medical University, India histologically confirmed seven bladder cancer patients were recruited from Department of Urology, Chhatrapati Shahuji Maharaj Medical University, Lucknow, India. Total RNA was extracted from tumor biopsies and hybridized on affymetrix Human Gene ST 1.1 array to determine differentially expressed genes in urinary bladder cancer with muscle invasion in comparison of normal human urinary bladder.
2012-02-22 | E-GEOD-23732 | biostudies-arrayexpress
Project description:36 cases of UCB and 29 adjacent normal bladder tissues (22 pairs) were derived from patients diagnosed with UCB and received radial cystectomy at Sun Yat-sen University Cancer Center (SYSUCC, Guangzhou, China).Total RNA was isolated using TRIzol® Reagent (Ambion). The RNA concentration and quality were determined with NanoDrop, Qubit and agarose gel analysis. The Dynabeads® mRNA Purification Kit (Ambion) was used to enrich the mRNAs, which were used as templates for RNA-BisSeq library construction. For RNA-BisSeq, bisulfite-treated mRNAs were first subjected to reverse transcription with ACT hexamers and Superscript II Reverse Transcriptase (Invitrogen), and the following processes were carried out with KAPA mRNA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions. The libraries were sequenced on the Illumina HiSeq X-Ten platform at Novogene (Tianjin, CA) with paired-end 150 bp read length. The m5C sites were called using meRanCall from meRanTK (FDR < 0.01). The differential m5C sites were detected and the hypermethylated m5C in UCB samples correlates with oncogene mRNA overexpression in UCBs.
2019-07-02 | GSE133622 | GEO
Project description:36 cases of UCB and 29 adjacent normal bladder tissues (22 pairs) were derived from patients diagnosed with UCB and received radial cystectomy at Sun Yat-sen University Cancer Center (SYSUCC, Guangzhou, China). Total RNA was isolated using TRIzol® Reagent (Ambion). The RNA concentration and quality were determined with NanoDrop, Qubit and agarose gel analysis. The Dynabeads® mRNA Purification Kit (Ambion) was used to enrich the mRNAs, which were used as templates for RNA-Seq library construction. RNA-Seq libraries was directly constructed by using KAPA mRNA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions. The libraries were sequenced on the Illumina HiSeq X-Ten platform at Novogene (Tianjin, CA) with paired-end 150 bp read length. The different genes expression between the UCB and adjacent normal tissues were detected. Several genes related to cancer pathways were dysregulated.
2019-07-02 | GSE133624 | GEO
Project description:RNA m5C analysis in human urothelial carcinoma of the bladder (UCB) and adjacent normal tissues.
| PRJNA552054 | ENA
Project description:Objectives: Much of the information to date in terms of subtypes and function of bladder urothelial cells were derived from anatomical location or by the expression of a small number of marker genes. To have a comprehensive map of the cellular anatomy of bladder urothelial cells, we performed single-cell RNA-sequencing to thoroughly characterize mouse bladder urothelium. Materials and methods: A total of 18,917 single cells from mouse bladder urothelium was analyzed by unbiased single-cell RNA sequencing. The expression of the novel cell marker was confirmed by immunofluorescence using urinary tract infections models. Results: Unsupervised clustering analysis identified 8 transcriptionally distinct cell subpopulations from mouse bladder urothelial cells. We discovered a novel type of bladder urothelial cells marked by Plxna4 that may be involved with host response and wound healing. We also found a group of basal-like cells labeled by ASPM that could be the progenitor cells of adult bladder urothelium. ASPM+ urothelial cells are significantly increased after injury by UPEC. In addition, specific transcription factors were found to be associated with urothelial cell differentiation. At the last, a number of interstitial cystitis/bladder pain syndrome-regulating genes were found differentially expressed among different urothelial cell subpopulations. Conclusions: Our study provides a comprehensive characterization of bladder urothelial cells, which is fundamental to understanding the biology of bladder urothelium and associated bladder disease.
2020-12-12 | GSE163029 | GEO
Project description:Analysis of urinary bladder in wild-type C57BL/6 females sacrificed every 4 hours at six time points under constant darkness after acclimation for 2 weeks under 12-hour light and 12-hour dark conditions. Results provide insight into circadian gene expression patterns in normal urinary bladder. Analysis of urinary bladder in wild-type C57BL/6 females sacrificed every 4 hours at six time points (n=2 for each time (CT 0, 4, 8, 12 and 20)) under constant darkness after acclimation for 2 weeks under 12-hour light and 12-hour dark conditions.
2012-04-30 | E-GEOD-35795 | biostudies-arrayexpress
Project description:We report the application of single-cell based sequencing for high throughput profiling of the mouse urinary bladder. By utilizing multiple dissociation techniques and library preparation techniques we generated an atlas comprising 43,119 cells including major cell types absent from previous reports. We found that previous single-cell profiling of the mouse bladder lacked a major cell type in the detrusor smooth muscle and incorrectly annotated other cell types such as mesothelial cells. Using the atlas, we elucidated aspects of bladder biology including urothelial differentiation, the identity of interstitial cells of Cajal, detrusor smooth muscle control and immune distributions. Finally, we combine the single-cell based sequencing with spatial transcriptomics and imaging mass cytometry to add spatial context to transcriptomic profiling.
2021-12-21 | GSE180128 | GEO